Minor patch

stracquadaniolab · Feb 19, 2024 · 094d98d · 094d98d
1 parent 664bfcd
commit 094d98d
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Showing 3 changed files with 9,179 additions and 3 deletions.
diff --git a/bin/openmm-runner.py b/bin/openmm-runner.py
@@ -8,8 +8,8 @@
 pdb = PDBFile(sys.argv[1])
 forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
 modeller = Modeller(pdb.topology, pdb.positions)
-#modeller.deleteWater()
-#residues=modeller.addHydrogens(forcefield)
+modeller.deleteWater()
+residues=modeller.addHydrogens(forcefield)
 solvmol=int(sys.argv[4])
 modeller.addSolvent(forcefield, numAdded=solvmol)
 system = forcefield.createSystem(modeller.topology, nonbondedMethod=PME, nonbondedCutoff=1.0*nanometer, constraints=HBonds)

diff --git a/nextflow.config b/nextflow.config
@@ -1,6 +1,6 @@
 // your workflow parameters
 params {
-  inputFile  = "./testdata/2JIE.pdb"
+  inputFile  = "./testdata/7f1n.pdb"
   resultsDir = "./results/"
 }